eke.biomarker


Nameeke.biomarker JSON
Version 1.1.25 PyPI version JSON
download
home_pagehttps://github.com/EDRN/eke.biomarker
SummaryBiomarkers for the EDRN Knowledge Environment
upload_time2017-06-23 17:14:43
maintainerNone
docs_urlNone
authorSean Kelly
requires_pythonNone
licenseALv2
keywords web zope plone edrn cancer biomarkers eke knowledge
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI
coveralls test coverage No coveralls.
            *************
eke.biomarker
*************

This product, ``eke.biomarker``, provides display and RDF_ ingest of the
biomarkers being studied by the Early Detection Research Network (EDRN_).
Biomarkers are chemical indicators for disease, and in the case of EDRN, the
disease being pursued is cancer.  This package lets a researcher browse,
search for, and discover interesting biomarkers, determine how research
progress is being made, find out statistical values of the biomarkers, and so
forth.  These features are integral to the EDRN Knowledge Environment (EKE_).
EDRN uses the EKE to make it easy to discover, share, search for, and retrieve
all of EDRN's collective knowledge, including cancers and other diseases,
protocols, specimens, participants, staff, and |---| as in the case of this
product |---| biomarkers.

Although intended for the EDRN public portal, it can be installed in any
Plone_ compatible site.

This software is developed by the `EDRN Informatics Center`_  at JPL_,
operated by the California Institute of Technology, for NCI_.

.. References:
.. _EDRN Informatics Center: http://cancer.jpl.nasa.gov/
.. _EDRN: http://edrn.nci.nih.gov/
.. _EKE: http://cancer.jpl.nasa.gov/documents/applications/knowledge-environment
.. _JPL: http://www.jpl.nasa.gov/
.. _NCI: http://cancer.gov/
.. _Plone: http://plone.org/
.. _RDF: http://w3.org/RDF/
.. |---| unicode:: U+2014 .. EM DASH


Installation
============

Use Buildout_ with the plone.recipe.zope2instance recipe.

• Add ``eke.biomarker`` to the list of eggs to install, e.g.::
 
    [buildout]
    ...
    eggs =
        ...
        eke.biomarker
        
• Re-run buildout, e.g. with::
  
    % ./bin/buildout
        
You can skip the ZCML slug if you are going to explicitly include the package
from another package's configure.zcml file.

.. References:
.. _Buildout: http://www.buildout.org/


Changelog
=========

What follows is a history of changes from release to release.  Where issue IDs
are listed below, you can find out more about them by visiting the issue
tracker at https://oodt.jpl.nasa.gov/jira/browse/CA.


1.1.25 — Follow the protocols!
------------------------------

• CA-1552: 200 character truncation of protocols causes ingest issue


1.1.24 — Fast ingestion aids digestion
--------------------------------------

• CA-1434: Id searching makes biomarker ingest take too long


1.1.23 — You're So Vain
-----------------------

• Add a "piUIDs" field to Biomarker objects and set it on ingest so that
  vanity pages can quickly find Biomarkers studied by a PI.


1.1.22 — Some Day We'll Get This Right
--------------------------------------

• CA-1454: Biomarker ingest should use the organs specified in the RDF to
  associate a biomarker with a collaborative group, not the security access
  group


1.1.21 — By Any Other Name
--------------------------

• CA-1348: Summary source URLs should be marked as required
• CA-1388: Pull external resource links from CancerDataExpo
• CA-1440: Biomarker ingest should accept "GI and Other Associated" as well as
  "G.I. and Other Associated"


1.1.20 — Protection
-------------------

• CA-1349: Summary ingest should be robust in the face of failures


1.1.19 — Visuals
----------------

• CA-1322
• CA-1338: Fix tests for eke.biomarker


1.1.18 — Biomuta
----------------

• Added External Resources through simply linking with HgncName. This is a 
  temporary hack, will add knowledge objects for each external resource.
• Added Biomuta tab to a Biomarker's elemental page and also removed biomuta 
  link from "basic" tab. Biomuta tab was not added to Panel since Biomuta entries
  reference single biomarker entities. Biomuta stats are added as an attribute 
  of a Biomarker since they are characteristics associated directly with the 
  biomarker. CA-1321.


1.1.17 — Bug Fixes
------------------

• CA-1300
• CA-1303


1.1.16 — Broken Links
---------------------

• This release addresses an RDF ingest issue where a biomarker-bodysystem object
  refers to a biomarker that doesn't exist.


1.1.15 — I Had Some Chicken; Pass Me the FLOSS
----------------------------------------------

• First official release as free/libre/open source software.


1.1.14 — Download URL
---------------------

This release specifies a full path to the download URL for this package.  This
is necessary since JPL now blocks directory listings of our distribution server,
and previously Python would use the directory listing to find the matching
file by version to download.


1.1.13 — Certified HGNNNNNNNC!
------------------------------

• CA-1235 - Make biomarkers link ID end with HGNC name
• CA-1238 - Add free text search to Biomarkers
• CA-1247 - Link back to BioMuta from EDRN Portal's biomarkers
• CA-1264 - Add Clinical Certification flags


1.1.12 — Let's Not Talk
-----------------------

• CA-1229 - Discussion re-enabled after upgrade


1.1.11 — Bio-TASTIC!
--------------------

• Adds the PIs-by-Biomarkers report plus a menu of (future) reports
• CA-1206 - "No resources" appears on a biomarker–body-system when there are
  no publications, not if there are no resources
• CA-1205 - Sort resources alphabetically on elemental- and panel-based
  biomarkers
• CA-1156 - Show more attributes for biomarkers that are "mostly public"
• CA-1163 - Make RDF ingest defensive against bad protocols from BMDB
• CA-1182 - Recognize "Private" QA State of Biomarker
• CA-1184 - Biomarker "report" by Organ
• CA-1189 - Enable left+right portlets on /biomarkers
• Drops the obsolete "Review Listing" type


1.1.10 — More Upgrades
----------------------

• Compatibility with Plone 4.3.
• Uses z3c.autoinclude.


1.1.9 — Get Him to the Greek
----------------------------

• CA-1100 Show "N/A" for Prevalence, NPV and PPV


1.1.8 — Lies, Damn Lies, and Statistics
---------------------------------------

* Made compatible with Plone 4.2.4.
* CA-1083 - eke.biomarker RDF ingest should treat predicate
  "hasBiomarkerStudyDatas" as a resource-pointing predicate
* CA-1090 - For biomarkers, show a "-" or "N/A" or SOMETHING for prevalence,
  NPV, and PPV if they're zero or not given.


1.1.7 — Upgrades
----------------

* Made compatible with Plone 4.1.5.
* CA-1010 - Show blank if values are 0 or 0.0


1.1.6 — Test Support
--------------------

This release includes:

* Depending on just Plone the framework instead of Plone the application.


1.1.5 — Dataset Linkages
------------------------

This release includes:

* CA-784: Add ability to associate eCAS datasets with Biomarker records in the
  BMDB
* (No issue ID): Dataset links should go directly into eCAS


1.1.4 — Resiliency: the bread and butter of PvP
-----------------------------------------------

This release makes functional tests more resilient.


1.1.3 — Let's Collaborate!
--------------------------

This release includes:

* A plone.app.testing layer.
* Support for edrnsite.collaborations
* Re-attaches biomarkers that indicate their collaborative group back to the
  "Collaborative Group" (from edrnsite.collaborations) objects to which they
  "belong".


1.1.2 — Upgrade Cleanup
-----------------------

This release updates the GenericSetup profile to 4, provides upgrade steps to
that profile, and makes the testing and development harness depend on "trunk"
level of other eggs instead of on released versions of those eggs.


1.1.1 — Unique IDs
------------------

This release replaces the unique ID generation method for "Study Statistics"
objects from the "generateUniqueId" method (acquired from who knows where
(possibly CacheFu?)) to UUIDs, the generation of which is part of the standard
library.


1.1.0 — Plone 4
---------------

This release of eke.biomarker makes it compatible with Plone 4.


1.0.2 — A Mixed Bag
-------------------

The following issues were addressed in this release:

* CA-620 - Locks appear on biomarkers listed under a protocol incorrectly
  (test exposure)
* CA-698 - "Structural" objects appear in searches


1.0.1 — Sweeping Views
----------------------

This release adds a number of improvements to the biomarker views to
reflect requests made by NCI that more specific details be captured in
each annotated biomarker.

This release addresses the following issues:

* CA-674 - Add PerformanceComment to the biomarker organ tab
* CA-675 - Portal: Change name of sensitivity/specificity and add specific assay type attribute
* CA-676 - Portal: Add decision rule attribute to biomarker-organ-study information


1.0.0 — Prime Time
------------------

This release addresses a number of issues 
that make this component (and some of its
selected counterparts) "prime time" for
the operational NCI portal. 

This release addresses the following issues:

* CA-528 Automatic periodic ingest of RDF

You can find the issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA


0.0.6 — Open Door Policy
------------------------

For this release, we're exposing more information about biomarkers.  Instead
of making unapproved biomarkers private and requiring a log in to view them,
you can now view basic information about them.  Full details require a login.
For more information, see https://oodt.jpl.nasa.gov/jira/browse/CA-650.


0.0.5 — Eleventh Hour
---------------------

This release includes some look-and-feel changes, specifically to support
https://oodt.jpl.nasa.gov/jira/browse/CA-600.


0.0.4 — Padlocked!
------------------

This release addresses the following issue:

* https://oodt.jpl.nasa.gov/jira/browse/CA-551 - Add lock icon to biomarkers
  and science data that are "secure" to protocol pages


0.0.3 — The unnamed release
---------------------------

* http://oodt.jpl.nasa.gov/jira/browse/CA-511 - Need to index alternative
  biomarker names


0.0.2 — Various "CYA" Fixes
---------------------------

* http://oodt.jpl.nasa.gov/jira/browse/CA-499 - Disclaimer needed on
  biomarker list.
* http://oodt.jpl.nasa.gov/jira/browse/CA-500 - Show unpublished
  biomarkers in a biomarker folder.
* http://oodt.jpl.nasa.gov/jira/browse/CA-510 - Lock box for science data and
  biomarkers should disappear if a user has access to the object


0.0.1 — Security Ingest
-----------------------

The sole issue addressed in this release is:

* http://oodt.jpl.nasa.gov/jira/browse/CA-475 - "Public" should only see
  biomarkers and science data that have QAState=Accepted.  Disregard Security
  flag.


0.0.0 — Unreleased
------------------

Initial release into beta.
            

Raw data

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These features are integral to the EDRN Knowledge Environment (EKE_).\nEDRN uses the EKE to make it easy to discover, share, search for, and retrieve\nall of EDRN's collective knowledge, including cancers and other diseases,\nprotocols, specimens, participants, staff, and |---| as in the case of this\nproduct |---| biomarkers.\n\nAlthough intended for the EDRN public portal, it can be installed in any\nPlone_ compatible site.\n\nThis software is developed by the `EDRN Informatics Center`_  at JPL_,\noperated by the California Institute of Technology, for NCI_.\n\n.. References:\n.. _EDRN Informatics Center: http://cancer.jpl.nasa.gov/\n.. _EDRN: http://edrn.nci.nih.gov/\n.. _EKE: http://cancer.jpl.nasa.gov/documents/applications/knowledge-environment\n.. _JPL: http://www.jpl.nasa.gov/\n.. _NCI: http://cancer.gov/\n.. _Plone: http://plone.org/\n.. _RDF: http://w3.org/RDF/\n.. |---| unicode:: U+2014 .. 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Where issue IDs\nare listed below, you can find out more about them by visiting the issue\ntracker at https://oodt.jpl.nasa.gov/jira/browse/CA.\n\n\n1.1.25 \u2014 Follow the protocols!\n------------------------------\n\n\u2022 CA-1552: 200 character truncation of protocols causes ingest issue\n\n\n1.1.24 \u2014 Fast ingestion aids digestion\n--------------------------------------\n\n\u2022 CA-1434: Id searching makes biomarker ingest take too long\n\n\n1.1.23 \u2014 You're So Vain\n-----------------------\n\n\u2022 Add a \"piUIDs\" field to Biomarker objects and set it on ingest so that\n  vanity pages can quickly find Biomarkers studied by a PI.\n\n\n1.1.22 \u2014 Some Day We'll Get This Right\n--------------------------------------\n\n\u2022 CA-1454: Biomarker ingest should use the organs specified in the RDF to\n  associate a biomarker with a collaborative group, not the security access\n  group\n\n\n1.1.21 \u2014 By Any Other Name\n--------------------------\n\n\u2022 CA-1348: Summary source URLs should be marked as required\n\u2022 CA-1388: Pull external resource links from CancerDataExpo\n\u2022 CA-1440: Biomarker ingest should accept \"GI and Other Associated\" as well as\n  \"G.I. and Other Associated\"\n\n\n1.1.20 \u2014\u00a0Protection\n-------------------\n\n\u2022 CA-1349: Summary ingest should be robust in the face of failures\n\n\n1.1.19 \u2014 Visuals\n----------------\n\n\u2022 CA-1322\n\u2022 CA-1338: Fix tests for eke.biomarker\n\n\n1.1.18 \u2014 Biomuta\n----------------\n\n\u2022 Added External Resources through simply linking with HgncName. 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CA-1321.\n\n\n1.1.17 \u2014 Bug Fixes\n------------------\n\n\u2022 CA-1300\n\u2022 CA-1303\n\n\n1.1.16 \u2014 Broken Links\n---------------------\n\n\u2022 This release addresses an RDF ingest issue where a biomarker-bodysystem object\n  refers to a biomarker that doesn't exist.\n\n\n1.1.15 \u2014 I Had Some Chicken; Pass Me the FLOSS\n----------------------------------------------\n\n\u2022 First official release as free/libre/open source software.\n\n\n1.1.14 \u2014 Download URL\n---------------------\n\nThis release specifies a full path to the download URL for this package.  This\nis necessary since JPL now blocks directory listings of our distribution server,\nand previously Python would use the directory listing to find the matching\nfile by version to download.\n\n\n1.1.13 \u2014 Certified HGNNNNNNNC!\n------------------------------\n\n\u2022 CA-1235 - Make biomarkers link ID end with HGNC name\n\u2022 CA-1238 - Add free text search to Biomarkers\n\u2022 CA-1247 - Link back to BioMuta from EDRN Portal's biomarkers\n\u2022 CA-1264 - Add Clinical Certification flags\n\n\n1.1.12 \u2014\u00a0Let's Not Talk\n-----------------------\n\n\u2022 CA-1229 - Discussion re-enabled after upgrade\n\n\n1.1.11 \u2014\u00a0Bio-TASTIC!\n--------------------\n\n\u2022 Adds the PIs-by-Biomarkers report plus a menu of (future) reports\n\u2022 CA-1206 - \"No resources\" appears on a biomarker\u2013body-system when there are\n  no publications, not if there are no resources\n\u2022 CA-1205 - Sort resources alphabetically on elemental- and panel-based\n  biomarkers\n\u2022 CA-1156 - 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Full details require a login.\nFor more information, see https://oodt.jpl.nasa.gov/jira/browse/CA-650.\n\n\n0.0.5 \u2014 Eleventh Hour\n---------------------\n\nThis release includes some look-and-feel changes, specifically to support\nhttps://oodt.jpl.nasa.gov/jira/browse/CA-600.\n\n\n0.0.4 \u2014 Padlocked!\n------------------\n\nThis release addresses the following issue:\n\n* https://oodt.jpl.nasa.gov/jira/browse/CA-551 - Add lock icon to biomarkers\n  and science data that are \"secure\" to protocol pages\n\n\n0.0.3 \u2014 The unnamed release\n---------------------------\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-511 - Need to index alternative\n  biomarker names\n\n\n0.0.2 \u2014 Various \"CYA\" Fixes\n---------------------------\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-499 - Disclaimer needed on\n  biomarker list.\n* http://oodt.jpl.nasa.gov/jira/browse/CA-500 - Show unpublished\n  biomarkers in a biomarker folder.\n* http://oodt.jpl.nasa.gov/jira/browse/CA-510 - Lock box for science data and\n  biomarkers should disappear if a user has access to the object\n\n\n0.0.1 \u2014 Security Ingest\n-----------------------\n\nThe sole issue addressed in this release is:\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-475 - \"Public\" should only see\n  biomarkers and science data that have QAState=Accepted.  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